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53 lines
1.7 KiB
YAML
53 lines
1.7 KiB
YAML
name: bwameth_index
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description: Performs indexing of c2t converted reference genome
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keywords:
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- bwameth
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- 3-letter genome
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- index
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- methylseq
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- bisulphite
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- fasta
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tools:
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- bwameth:
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description: |
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Fast and accurate alignment of BS-Seq reads
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using bwa-mem and a 3-letter genome.
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homepage: https://github.com/brentp/bwa-meth
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documentation: https://github.com/brentp/bwa-meth
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arxiv: arXiv:1401.1129
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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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input:
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- fasta:
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type: file
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description: Input genome fasta file
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output:
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- index:
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type: file
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description: c2t converted genome BWA index files
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pattern: "*.{bwameth.c2t.amb,bwameth.c2t.ann,bwameth.c2t.bwt,bwameth.c2t.pac,bwameth.c2t.sa}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@phue"
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